src/brains/BlockSnapshotManager.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#ifndef BRAINS_BLOCKSNAPSHOTMANAGER_HPP
#define BRAINS_BLOCKSNAPSHOTMANAGER_HPP
#include <vector>

#include "brains/SnapshotManager.hpp"
namespace OpenMD {

  class SimInfo;
  class DumpReader;

  typedef std::pair<int, int> SnapshotBlock;

  /**
   * @class BlockSnapshotManager
   * @todo document
   */
  class BlockSnapshotManager : public SnapshotManager{

  public:
    BlockSnapshotManager(SimInfo* info, const std::string& filename, int storageLayout, long long int memSize, int blockCapacity = 2);
    ~BlockSnapshotManager();
        
    virtual Snapshot* getSnapshot(int id);


    /** Returns number of snapshot blocks in this BlockSnapshotManager*/
    int getNBlocks() {
      return blocks_.size();
    }

    SnapshotBlock getSnapshotBlock(int block) {
      return blocks_.at(block);
    }
        
    int getNActiveBlocks();

    void needCOMprops(bool ncp);


    bool isBlockActive(int block) {
      return  findActiveBlock(block) != activeBlocks_.end() ? true : false;
    }        

    bool loadBlock(int block);
        
    bool unloadBlock(int block);

    std::vector<int> getActiveBlocks();

    int getBlockCapacity() {
      return blockCapacity_;                
    }

    int getNFrames();
        
  private:

    std::vector<int>::iterator findActiveBlock(int block) {
      return std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
    }

    bool hasZeroRefBlock();

    int getFirstZeroRefBlock();

    void internalLoad(int block);
    void internalUnload(int block);
    Snapshot* loadFrame(int frame);
        
    SimInfo* info_;
    int blockCapacity_;
    long long int memSize_;

    std::vector<Snapshot*> snapshots_;
    std::vector<SnapshotBlock> blocks_;        
    std::vector<int> activeBlocks_;
    std::vector<int> activeRefCount_;
        
    int nAtoms_;
    int nRigidBodies_;
    int nCutoffGroups_;
    
    DumpReader* reader_;
    int nframes_;
    int nSnapshotPerBlock_;

  };

}

#endif
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	4148 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	tim	318	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	318	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	318	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	318	*/
42			#ifndef BRAINS_BLOCKSNAPSHOTMANAGER_HPP
43			#define BRAINS_BLOCKSNAPSHOTMANAGER_HPP
44	tim	323	#include <vector>
45	tim	318
46			#include "brains/SnapshotManager.hpp"
47	gezelter	1390	namespace OpenMD {
48	tim	318
49	gezelter	507	class SimInfo;
50			class DumpReader;
51	tim	318
52	gezelter	507	typedef std::pair<int, int> SnapshotBlock;
53	tim	318
54	gezelter	507	/**
55			* @class BlockSnapshotManager
56			* @todo document
57			*/
58			class BlockSnapshotManager : public SnapshotManager{
59	tim	318
60	gezelter	507	public:
61	gezelter	1596	BlockSnapshotManager(SimInfo* info, const std::string& filename, int storageLayout, long long int memSize, int blockCapacity = 2);
62	gezelter	507	~BlockSnapshotManager();
63	tim	318
64	gezelter	1249	virtual Snapshot* getSnapshot(int id);
65	tim	318
66	xsun	1215
67	gezelter	507	/** Returns number of snapshot blocks in this BlockSnapshotManager*/
68			int getNBlocks() {
69			return blocks_.size();
70			}
71	tim	318
72	gezelter	507	SnapshotBlock getSnapshotBlock(int block) {
73			return blocks_.at(block);
74			}
75	tim	318
76	gezelter	507	int getNActiveBlocks();
77	tim	351
78	gezelter	1106	void needCOMprops(bool ncp);
79
80
81	gezelter	507	bool isBlockActive(int block) {
82			return findActiveBlock(block) != activeBlocks_.end() ? true : false;
83			}
84	tim	351
85	gezelter	507	bool loadBlock(int block);
86	tim	318
87	gezelter	507	bool unloadBlock(int block);
88	tim	318
89	gezelter	507	std::vector<int> getActiveBlocks();
90	tim	318
91	gezelter	507	int getBlockCapacity() {
92			return blockCapacity_;
93			}
94	tim	318
95	gezelter	507	int getNFrames();
96	tim	318
97	gezelter	507	private:
98	tim	318
99	gezelter	507	std::vector<int>::iterator findActiveBlock(int block) {
100			return std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
101			}
102	tim	351
103	gezelter	507	bool hasZeroRefBlock();
104	tim	351
105	gezelter	507	int getFirstZeroRefBlock();
106	tim	351
107	gezelter	507	void internalLoad(int block);
108			void internalUnload(int block);
109			Snapshot* loadFrame(int frame);
110	tim	318
111	gezelter	507	SimInfo* info_;
112			int blockCapacity_;
113	gezelter	1596	long long int memSize_;
114	tim	318
115	gezelter	507	std::vector<Snapshot*> snapshots_;
116			std::vector<SnapshotBlock> blocks_;
117			std::vector<int> activeBlocks_;
118			std::vector<int> activeRefCount_;
119	tim	318
120	gezelter	507	int nAtoms_;
121			int nRigidBodies_;
122	gezelter	1782	int nCutoffGroups_;
123	tim	318
124	gezelter	507	DumpReader* reader_;
125			int nframes_;
126			int nSnapshotPerBlock_;
127	tim	318
128	gezelter	507	};
129	tim	318
130			}
131
132			#endif